Download manual
Here you can download the EDGAR manual... or what comes closest to it
Actually, there is no EDGAR manual, but all features of the web interface are explained in the "Features" section of this EDGAR web page.
For further reading, there is the first EDGAR publication from 2009 which can be found here:
EDGAR - A software platform for comparative genomics
Another valuable source is the PhD-thesis of Jochen Blom, which is not about EDGAR alone, but more up-to-date and more comprehensive:
Comparative genomics on gene and single nucleotide level
The most up-to-date reference is the EDGAR 2.0 publication from 2016 which can be found here:
EDGAR 2.0: an enhanced software platform for comparative gene content analyses.